Into the Darkness
by Keva08
Summary: When there is beauty in the world you must discover it, when there is evil in the world you must fight it. A mysterious Commander offers her assistance to Kirk and the Enterprise, to capture their target, John Harrison. Who is this woman and how will she effect the course of history? Spoilers Star Trek Into Darkness.
1. Chapter 1

Welcome everyone. Please read and review. I am trying to do this story from memory of what happened in the new movie, so please be patient. I don't know how often this will get updated, hopefully once a week, but I am extremely busy this summer.

The characters and worlds belong to their creators and owners. I do own Charlie Archer.

Please Read and Review, it will help me update faster with encouragement.

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"Move! Clear the way! Make a hole!"

The people in the hall flattened themselves to the wall or jumped out of the way, as a figure ran past.

The sound of fast moving feet brought the attention of the man at the desk to the figure that came flying into his office.

"Sir, we've found him."

The head of Starfleet, Admiral Marcus, stood and demanded, "Where?"

"London, Sir. Surveillance puts him outside The Achieves just before the explosion."

"Got you, you son of a bitch! Get me everything you have on him and the explosion, but nothing to do with Sector 31. Then initiate protocol, recall everyone. We need to hunt this bastard down."

"Yes, Sir."

"Oh, and Commander, you're my expert on him, you're with me at the briefing."

"Yes, Sir."

The Commander left, no longer running but with haste to carry out their new orders, all the while muttering under their breath, "Khan, what are you planning?"

* * *

As the last of the command staff filed into the room, a lone figure surveyed them. Each person represented the elite that Starfleet had to offer, but the figure had an ominous feeling that they wouldn't be enough to stop whatever plan Khan was about to unleash.

Unlike Admiral Marcus, Commander Charlotte "Charlie" Archer, did not underestimate what Khan could and would do for revenge.

"Come to order," Admiral Marcus called to those who had assembled. Each was seated but one chair was left open at Marcus' right side.

"Ah, Commander Archer, glad that you could join us."

The petite Commander moved out of the shadows and took the lone open seat.

"Good evening everyone, thank you, for being prompt. Our intelligence has identified our target… His name is John Harrison and he's one of our own."

Commander Charlotte Archer tuned out Admiral Marcus as she was already familiar with the information and instead focused on the image of John Harrison. How one man could be so destructive she wished she had never known, but she knew Khan and his history. Not that she could tell anyone, she was sworn to secrecy.

She refocused on the room as the infamous Captain, now Commander James T. Kirk, asked the most important question… why?

"Could just be the beginning."

Charlie decided to jump into the conversation, "I conquer with Commander Kirk, if Harrison wants war with Starfleet, the bombing was just the beginning."

Marcus looked annoyed that she had actually agreed with Kirk. She could see him trying to figure out what her play was, but with her training it was near impossible.

Suddenly Charlie felt a cold shiver go down her spine, the one she always got when Khan was close. She surveyed the door; wherever he was he was close. She was about to interrupt further when a blinding light flooded the room. A jump ship had moved into position just outside of the window. Kirk had enough time to realize their target was the pilot and to yell for everyone to clear the room, before the occupant of the ship opened fire.

She threw herself under the table, cursing both Khan and herself for her failure to bring a weapon other than her concealed knife. The sound of weapons fire and screaming brought her focus back to those who were not so lucky to get out of the target range.

Four were dead with three injured; she could hear Admiral Christopher Pike calling for back up. Admiral Marcus wasn't anywhere to be found.

'Coward,' her mind roared. The man had unleashed this monster, took the one thing he cared for most, and then lost control of him, leaving the unsuspecting Starfleet officers to pay the price.

If she didn't need Marcus and his resources to capture Khan, she would have been half tempted to shoot the bastard herself. She moved to check a prone figure, she may not have a weapon but she could move the injured to safety.

Dead. It was unfortunate; she had liked the eager Commander Hopper.

She moved on and turned to see Commander Spock dragging a figure out of the room. She rushed after and found the Commander at the side of Admiral Pike, who was obviously struggling to breath due to his wounds.

"Shit."

Charlie rushed forward to help but it was clear that he wouldn't last long without medical attention. She didn't even flinch at the sound of an explosion and a crash.

All she was focused on was the man slowly dying in front of her. She grabbed his hand to give what comfort she could. She murmured nonsense and reassurances, she had only met the man twice but she knew his history. What he had done for Starfleet and during the Nero incident.

Commander Spock seemed frozen, stunned to see the Admiral gasping for breath. He then did something odd; he formed a mind-meld with the dying man and maintained it as Pike succumbed to his wounds.

Charlie was just as shocked to see a pillar of Starfleet fade before her eyes. There was movement behind them and Kirk dropped to his knees, a look of pure disbelief on his face. He reached to check what she already knew Pike was gone.

She felt her heart break as the young Captain gave into his emotions. She had heard how close they were and it was hard to watch as a fellow officer mourned for his fallen mentor.

Spock remain stoic and blank faced, but having known Vulcans her entire life, Charlie could see the struggle the Commander was having, trying to repress the tidal wave of emotions threatening his control.

She sat silently watching as Kirk regained control and moved off to mourn or plan his revenge she didn't know or care which.

Spock remained at Pike's side and closed his eyes, as a sign of respect. Then he too moved off but when he turned back to thank the female Commander for her assistance, he only saw the fading light of a transporter but no Commander or Pike in sight.

* * *

As the light of the transporter fade the female figure struggled under the weight of the body of her male companion.

"Doc, "she yelled. She heard someone moving quickly toward her from the front of the ship.

"Charlie?" the man questioned.

"Doc, give me a hand getting him up on the bed."

Together they moved the man onto a bed.

"Who is this? What the hell happened?"

"Doc, I'd like you to meet the man you're going to save. Admiral Christopher Pike."

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	2. Chapter 2

Hello everyone, thank you some much for your interest in this story and only after one chapter.

For everyone who is hoping that Pike will be in the story, he will, BUT this will mostly follow what happened in Into Darkness.

As always the characters and worlds belong to their creators and owners.

Please Read and Review!

* * *

Commander Charlie Archer stood in the background as Admiral Marcus met with the heads of the Starfleet divisions, trying to track down John Harrison. She had been up all night first with assisting the Doctor in reviving and stabilizing Pike and then trying to gather intelligence about the incident and where the Khan might have slipped off to.

She wasn't stupid, she knew Kahn was long gone; he had accomplished what ever goal and was now waiting to see what they would do. She just hoped that Marcus and anyone in Starfleet for that matter wouldn't do something incredibly stupid. Many had lost friends and commanding officers in the Achieves' explosion and the attack. It was human nature to seek revenge against those who had wronged you and those you loved, Khan knew his enemy well, playing on emotions to get what he wanted. Charlie just hoped it would not escalate to all out war.

Just thinking about Admiral Marcus and what he had done, stirred her own need for vengeance. His planning and scheming, not to mention his cowardly retreat during the attack, made her sick to her stomach that he was in such a highly respected position of power.

Marcus had woken a dangerous predator from its sleep and when it slipped its cage, he allowed innocent men and women become causalities in the aftermath of his arrogance. She couldn't believe the smug look the man had on his face when she had returned to duty. She didn't have the patience or the restraint to deal with him, so she avoided him as much as possible. That is until she was dragged into the debriefing along with the next of Starfleet's commanding officers. Sometimes being the expert on 'John Harrison' was a real bitch.

Charlie rolled her eyes at the assembled Starfleet Admirals, there was nothing that the stuck up, ignorant, and for lack of a better description pricks would or could do to stop Khan. The truth was Khan didn't need his superior intelligence or even strength to outwit and beat Starfleet. It was unfortunate but Starfleet had been woefully unprepared for the Nero incident and it seems still hadn't learned its lesson. Starfleet as a whole thought itself invincible but the hard truth that was sinking in was Starfleet trained explorers not soldiers to face the ever circling enemy.

Charlie knew what was out there and she cringed at the thought of the unprepared and untrained Starfleet members coming face to face with the evil and darkness that laid in wait out in the universe. She would never admit to anyone but she did agree with Marcus that Starfleet needed to learn how defend itself, but not by starting a full scale war with a rival power in the quadrant like the Klingons. Sometimes she found herself agreeing with Khan's assessment of humans, in which humans strived for peace and prosperity but still craved chaos and strife.

* * *

Charlie shook herself; her mind had wandered and she needed to focus but it was hard with the two sides of her brain were warring with each other. She was struggling between her training and what her heart and head told her. There were enemies of Starfleet everywhere both inside and out. She fought to remain loyal to the ideals of Starfleet while it was rotting from the top down. She also struggled with fighting the outside enemy, she could sympathize with Khan's rage at being thrown into another time and losing your crew, but he had to be stopped. She had to choose to fight the lesser of two evils head on and undermine the power of the other. There was no doubt that Marcus and Khan were both monsters in their own unique ways. Charlie assessed each and had to choose to fight the visible and immediate threat of Khan while working in the shadows to stop Marcus. She had to save the Earth and Starfleet from Khan so she could stop Marcus before he destroyed them both from the inside.

Charlie heard a commotion at the door and two men came bursting through the door at a dead run. They were as opposite as night and day, and then she realized who had the balls to interrupt a high ranking, classified meeting. She hid a smirk; of course Kirk and Spock would be the first to figure out where Harrison had gone, with the help of their loyal crew no doubt.

"Sir, he's not on Earth."

Marcus seemed to stare at them trying to decide whether it was worth it to hear them out. Charlie was willing to bet that the calculating look on Marcus' face meant nothing good for the pair and the crew they represented.

"Give us a minute."

The room began to clear of personal, but Archer stayed where she was. There was no way in hell she was going to allow Marcus to send these men and their crew on a suicide mission just to satisfy his need for blood.

Marcus glared at her, Charlie could see that he wanted to dismiss her, but she also knew that he wouldn't. Not if the smug bastard valued his dark and dirty little secrets. She knew where his skeletons were buried and had enough evidence currently on her person to have him shot where he stood. She gave him an innocent smile, just to piss him off more. She had no love for a man who had no loyalty to those he served with and who would send innocents to die as payment for his sins.

She didn't approach the three men, but stayed back to observe the interaction, assessing her enemy and the potential allies that were now caught it his web.

She watched as Marcus spilled one of his secrets in half lies and twisted truths. She had known the man was a snake when she met him but she never believed he would go this far to cover his ass.

"You park yourself on the edge of the neutral zone and fire a torpedo and then get the hell out of there."

She could not believe her ears when she finally heard what Marcus was suggesting or the fact that Kirk seemed to agree to the orders.

"Sir, I request Commander Spock be reinstated as my first officer."

Marcus seemed to pause and eyed the Commander up and down; whatever he was planning seemed to fall into place. Charlie had a feeling of dread when he agreed so easily.

"Alright."

Charlie didn't know what Marcus had planned but she couldn't sit by and leave Kirk and the Enterprise to face Marcus and Khan alone. She quickly stepped forward placing herself between her newly chosen allies and Marcus. The two men behind her may not have known the significance of the move but Marcus did. Charlie had just firmly shown that she try to protect the crew of the Enterprise against whatever Marcus had planned.

"Sir, I request to be reassigned to the Enterprise."

Marcus made to object obviously not liking that Charlie was trying to hinder his plans. But Charlie knew how to manipulate circumstances to her benefit and she moved in for the kill.

"You said so yourself, Sir, I am the expert on the target. I would be of more use to Captain Kirk than stuck here on Earth."

She knew she had won when Marcus' left eye twitched, it was his tell. Marcus eyed Charlie with what she would almost call respect, for the maneuvering she had just accomplished. She nodded politely to Marcus a smirk firmly in place as she followed her new Captain and first officer out of the monster's cave.

Both men paused just outside the office and turned to look at their new crew member, Charlie could see them both trying to figure out what they had just witnessed. Charlie turned her smirk into what some might call an innocent smile; it wouldn't do for her new commanding officers to think she had just enjoyed pissing off the highest ranking Starfleet officer, and that she was planning the many ways she could inflict harm on him if he threatened her or her newly adopted crew.

Charlie decided she had had enough of being within 100 yards of Marcus for the day, she felt liked she needed to take a long hot shower to clean off the ugly feeling she always had around him. She turned to the two curious men and prompted them with, "Shall we begin, Captain?"

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	3. Chapter 3

Hello everyone, thank you to all those who favored, followed, and read. I am encouraged to see that so many want to know what happens next.

I am trying a new point of view in this chapter, let me know what you think... I may or may not continue alternating POVs.

As always the characters and worlds belong to the creators and owners. I only own Commander Charlie Archer.

Please Read and Review!

* * *

**KIRK POV**

Kirk fell into step behind his newly reinstated first officer and the female Commander who had just bullied her way onto his ship. He remembered her from the previous night, though the blood and soot was gone. She was a mystery, he had never heard of her and he certainly would have remembered meeting her. Kirk glanced her over: petite, about 5'5" with blond hair tied into a bun at the back of her head. She was a classic beauty with blue eyes, full lips, and an hour glass figure. She walked with confidence, having no trouble keeping up with Spock's longer stride. Oh yes, Jim Kirk would definitely remember if he had ever met the little spit fire.

Kirk had not missed the interaction between the Admiral and the Commander. It was like watching to alpha wolves fighting for dominance, circling each other to see who would show weakness first. The Commander had obviously won the little power struggle, if the near devious smirk that had been on her face was anything to go by. He just wasn't sure what her goal was other than to piss Marcus off and that made him uneasy. He knew little about her or her background, she could prove to be truthful and be an asset in capturing Harrison or she could prove to be a distraction and spy for Marcus, he wouldn't put it past the Admiral, or she could even be working with Harrison.

"What exactly makes you an expert on John Harrison, Commander?"

The Commander slowed down to allow Kirk to catch up with them before she answered.

"I worked with him on various projects and was his partner on several missions. I am probably the closest person you will find that Harrison doesn't consider just an acquaintance or an enemy."

Kirk could tell the Commander was being truthful but she seemed to leave a lot unsaid.

"And which one would he consider Admiral Marcus to be?"

"Enemy."

The Commander didn't even pause to think on the answer, and that both confirmed Kirk's own theory and worried him even more. He knew he had just placed himself and his crew between two men who would tear apart the universe to reach their goal, whatever the means and whatever the cost.

"What is your assessment of Harrison, having worked so closely with him?"

The group came to a stop as the Commander turned to face Kirk, several emotions flashed across her face, before her face went blank.

"John Harrison is probably to most dangerous, intelligent, and ruthless man you'll ever meet and should not under any circumstances be underestimated. Whatever his goal is, he will do anything, destroy anything to achieve it. Captain, you have just painted a bulls-eye on your ship, whether we succeed or fail someone will be coming for us."

Kirk heard and understood the Commander's unspoken warning, never trust you enemy but never trust a man who just ordered you on a potential suicide mission, with a smile on his face. Obviously the Commander thought that Admiral Marcus was just as much of a threat as Harrison. Kirk agreed with the Commander that he didn't trust Marcus but he wouldn't go so far as to believe that Marcus would deliberately sabotage that mission that would bring an enemy of Starfleet to justice.

The Commander had remained silent after her statement, as if she was evaluating Kirk and his reaction. She finally nodded and Kirk got the feeling that he had just passed some test, what the test was he wasn't sure.

The group separated, each officer had duties to tend to before the Enterprise left on its mission.

Kirk paused to watch as the Commander slipped into the crowd and seemed to disappear. He would have to watch her closely, whether she proved to an ally or enemy was unclear only time would tell.

* * *

**Charlie POV**

"What's up Doc?"

Charlie grinned to herself when she heard the Doctor muttering on the other end of the communicator. She shouldn't tease him but after the day she had so far she needed some levity.

"Nothing is up, Charlie. But our patient is currently stable and beginning the recovery process."

Charlie sighed in relief, there had been at least three times the night before where she thought they had lost Pike for good. His heart had stopped twice and he had had a massive seizure, to hear that he had remained stable and was beginning the process of healing was the best news she had heard all day.

"Has he regained consciousness?"

"No, but I wouldn't expect him to between the massive blood loss, his heart stopping, and the drugs, his body has been through hell and has shut down to let itself recover. More good news, I was able to repair some of the damage to his spinal tissue and nerves. Should he make a full recovery he may thank you before court marshaling you for violating the Pri…"

"Yeah, I got it Doc, but he would be alive and kicking, that's the important part."

Charlie could practically hear the Doctor's scowl coming through the communicator. He seeming decided to drop the topic of her looming court marshal and asked for an update of his own.

"Anything new on where Harrison slipped off to?"

The Doctor knew that Harrison was Khan but Charlie was extremely thankful that he knew not to use Khan's real name when they were conversing in public. Especially as she was in a packed transport on her way to her apartment to gather what she would need for the trip.

"Qo'nos." _(Kronos)_

"Qo'nos? As in the Klingon home world?"

"Yup."

"And how exactly did he manage to get himself there? I've been monitoring the warp signatures coming and going from Earth, there is nothing around the time of the attack."

"He had a portable beaming transmitter. You should have seen that look on Marcus' face when Kirk told him where Harrison was and how he got away."

Charlie chuckled at the memory; Marcus' face would have made her day if it hadn't been the fact she was trying to prevent Kirk and Spock from accepting a suicide mission.

"Beaming device, I didn't think the prototypes were anywhere near ready for trials"

"Yeah, well Harrison must have built a separate one in secret and concealed it from Marcus."

The and me part of the sentence Charlie left unsaid. She knew she had screwed up; she had been meticulous at making sure she knew what Khan was working on and how far it was from completion. She had even sabotaged some of the projects to force delays and setbacks to prevent Marcus from getting his hands of the destructive creations Khan's mind managed to conjure. Khan knew she watched him closely, she hoped he assumed it was at Marcus's bidding not her own mission to trying to prevent Starfleet from gaining technology and weapons that it was not ready for. Khan's creations were meant for war and Charlie did and would do anything in her power to prevent it.

Charlie waited to see how long it would take the Doctor to catch the name she had dropped. She wasn't disappointed as the next words out of the Doctor's mouth were what she expected.

"Charlie what are you planning?"

She grinned; he knew her all too well and was probably imagining the craziest plans and worst possible outcomes. Even if it was a likely suicide mission especially with Marcus looming in the background, Charlie knew she couldn't leave Kirk and the Enterprise to fend for themselves.

"Marcus reassigned me to the Enterprise, to help Kirk track down Harrison."

She could hear a muffled snort come from the Doctor.

"There is no way in hell, Marcus actually willingly reassigned you."

Oh yes, the Doctor knew her very well indeed.

"I may have persuaded him, I am the foremost expert in Harrison after all."

"You just wanted to piss him off."

Charlie had to smother a giggle; she could practically hear the Doctor rolling his eyes at her antics.

"Well that too. It's a win/win situation. Hunt down and stop Harrison, piss off and ruin any and all of Marcus's plans. I say that's all in a day's work."

"Charlie just be careful, whatever Harrison and Marcus have planned for each other, means nothing good the ones caught in the middle."

Charlie let the mirth slip away becoming serious and focused on the mission that lay before her, the chances of actually succeeding were remote. Even if they managed to destroy or even capture Khan, Marcus was still planning something.

"I will Doctor, but I can't let Kirk take the Enterprise on a suicide mission when I can help tip the scales in their favor. This crew is up against two men hell bent on revenge, destruction, and war. They don't even know the true danger they are putting themselves in going after Harrison or trusting Marcus. Both have to be stopped and our best chance is with Kirk and the Enterprise on our side to help."

"Do what you feel you must, but Charlie remember your oaths, you can only do so much before you too become what you are trying so hard to stop."

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	4. Chapter 4

Hello everyone, thank you so much for reading, favoring, alerting, and reviewing.

As always the characters and worlds belong to the creators and owners. I own Charlie.

Please Read and Review!

* * *

Charlie had arrived to the shuttle before Kirk or Spock and had seated herself in the second row. The reports on the attacks had been filtering in and she was currently hunched over her padd trying to analyze the information and find something that had been missed. Anything that could give her the edge over Khan, Marcus, or even Kirk would be needed.

Khan and Marcus were her enemies, but Kirk was the unknown. Charlie couldn't get a good read on him and how he would react when all the pieces of the puzzle were finally revealed. He was a true believer in what Starfleet stood for and to have those ideals tarnished by Marcus, his superior and someone he was supposed to be able to trust, would force him to choice what kind of Captain he would be. The arrogant, playboy mask he wore could fool a lot to people, but Charlie knew that behind the mask lay intelligence, compassion, loyalty, and moral compass of what's right and wrong. Charlie had read about what he had done to become the Captain of the Enterprise, provoking Spock into a confrontation and using Spock's very nature against him, while not the smartest plan in the universe, it served a purpose. Kirk did not use Amanda Grayson's death against Spock just to be cruel and just take control, but prove a point and make the call that no one had the courage to do, face Nero head on in a battle that was impossible to win. But look what happened and what was accomplished: Earth was saved; Kirk, Spock, and the Enterprise were beginning their adventure.

Yes, Kirk was the wild card and Charlie would have to be careful.

The reports Charlie had spent the last few hours reviewing were the standard bullshit that Starfleet put out when they didn't know how or why something had occurred. Charlie quickly scrolled through the meaningless lines of dialogue, all saying the same thing: we don't know why or how it occurred, but Harrison successfully attacked two important and strategic points of Starfleet and managed to escape. She was looking for what Marcus didn't want to be seen or found, the missing pieces of information and classified portions of the reports. Charlie rolled her eyes that the Starfleet security software Marcus had his secret little minions create; she could break the code in less than a minute, but why waste her time when she could just use Marcus's personal code and password.

* * *

The reports held no new information that would help in Charlie's quest to stop Khan and Marcus. She was just about to hack the Section 31 mainframe when she was interrupted.

"Excuse me."

Charlie glanced up from her padd to see who had broken her concentration: male, tall, dark hair, science officer by his blue uniform, and focus in medicine by the med-kit he held under him arm.

Charlie shifted allowing the man to pass. He sat two seats over and placed his med-kit between them, pulling out a scanner and leaning forward between the seats in the next row.

It was then that Charlie realized that shuttle had begun to fill with other occupants and her new Captain and First Officer were sitting in front of her.

The man next to her continued his scans, replacing one instrument to pick up another. He obviously knew Kirk, as the blond Captain shot him a look of annoyance but didn't stop him.

Charlie found the interplay between Kirk and Spock fascinating. One dictated by logic the other by instinct. One reserved the other bold. One following his head, the other following his heart.

Charlie could see that their friendship was still forming; they were still trying to understand each other. They were completely opposite from one another but were two sides of the side coin, they just couldn't see it yet.

Spock was currently reminding Kirk that no man should be executed without a trial, even if his guilt was obvious. Charlie wondered which side Kirk would win out, the need for revenge or the need for justice.

"Bones, get that thing off my face."

Charlie grinned and then realized who was sitting next to her. The famous Leonard 'Bones' McCoy, another important piece to the Enterprise family and the only man who could balance Spock and Kirk's need to goad one another while keeping them on task. While Charlie wasn't a medical doctor she had great respect for Doctor McCoy and his accomplishments, plus dealing with Kirk for 4 years at the Starfleet Academy and then having to deal with both Kirk and Spock, anyone who could do that and survive almost mentally stable was a walking saint as far as Charlie was concerned.

* * *

There was movement at the entrance of the shuttle and Charlie caught a glimpse of blond hair and a blue science uniform and began cursing under her breath in every language known to man and a few that weren't. Charlie couldn't believe that Admiral Marcus would send his own daughter on a suicide mission; the man had reached an all time low.

"Captain Kirk?"

If Charlie hadn't been so pissed off she would have found it funny that at two simple words all males in the shuttle turned to face the pretty blond. Kirk, Spock, and McCoy were no exception. What came out of the woman's mouth shocked Charlie and secretly pleased her as well, not that she would ever tell anyone that.

"Science Officer Wallace, I've been assigned to the Enterprise by Admiral Marcus."

Well hell, seems daddy doesn't know his pride and joy was sneaking out and taking a joy ride around the galaxy with the universe's biggest playboy. Charlie was sure she was grinning like a mad woman, oh if she could see Marcus's face when he found out what Carol had done.

Though Carol had probably just made her day, that didn't mean that Charlie would let the woman off the hook. Charlie knew exactly why Carol was trying to get abroad the Enterprise and she would be having a little chat with her as soon as they were alone.

"These are my transfer orders."

Charlie rolled her eyes she could just imagine the look on Kirk face as he reviewed the orders.

"You requested an additional science officer, Captain?"

Charlie could have sworn she heard a little bit of hurt in Spock's question but she was probably just imagining things.

"I wish I had."

Ah, there was the famous Kirk bravado and wit.

"Lieutenant Carol Wallace, doctorate in applied physics, specializing in advanced weaponry."

Charlie would have laughed if it wouldn't have drawn attention, Carol looked very uncomfortable with Kirk reading her credentials, and Spock and McCoy were both leaning forward trying to see if they could get any more information.

"Impressive credentials."

Charlie could almost hear some respect in Spock's words.

"Thank you."

"But redundant now that I am back aboard the Enterprise."

And who said Vulcans couldn't be jealous or arrogant.

"And yet the more the merrier, have a seat Doctor."

Charlie could hear the unease in Kirk's words, seems that her new Captain wasn't as trusting as he may seem. Good, though Charlie, that will help keep us all alive a little longer.

Carol sat between the two men and Charlie just rolled her eyes, this was going to be a long mission, between Kirk and Spock and between Kirk and Carol. Charlie just hoped they would stay on mission long enough to stop whatever Khan and Admiral Marcus had planned.

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	5. Chapter 5

Hello everyone, sorry for the delay. As always I own nothing, but Charlie.

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* * *

Charlie was the last to disembark from the shuttle and she got her first real look at the legendary Enterprise. The loading bay was a bee hive of activity; everything was bright, sleek, and shiny. She made to follow Kirk and the other officers but was stopped by a large object being hoisted to the level above.

Charlie had to stop herself from snorting at the design and size of the torpedo, 'men always making things bigger to over compensate.' The torpedo was secured and she was free to follow the group. They hadn't gotten very far, and she watched as Kirk tried to reason with a man in a red uniform.

The man's accent sparked Charlie's memory, the infamous Montgomery Scott better known as 'Scotty' to his friends. She couldn't help but grin as Scotty ignored the weapons officer waiting for his signature, while he complained to Kirk. Charlie could see Scotty getting more and more worked up as Kirk didn't seem to share his opinion on the dangers of having unknown weapons of mass destruction on the ship.

"I'm not signing until I know what fuel these things have but he says," Scotty just points over his shoulder to the weapons officer behind him and the man answers on cue, "It's classified."

"It's classified," Charlie could hear the disbelief and irritation in the engineer's voice as he was being denied the information, "Then they won't be on the ship."

Charlie let Kirk deal with his upset Engineer, while she was no expert she had been there when Khan had been the early stages of designing the torpedoes and she was fairly certain he had been smart enough to build them so they wouldn't cause any problems. Although he probably hadn't planned on them being used to blow he and the planet he was on out to the sky.

Kirk and Scotty moved off and the torpedoes were loaded under Kirk's orders. Charlie scanned the hanger and found her target, a petite blond who was to curious for her own good.

Charlie grabbed the woman by the arm and dragged her away from the torpedo she was scanning.

"Lieutenant, let's have a little chat, shall we."

"Charlie… I mean Commander Archer, what are you doing here?"

"I could ask you the same thing Lieutenant Wallace."

Charlie watched as Carol winced at the name and knew she had been caught.

"I… well I… the torpedoes."

Charlie took pity at the woman's floundering.

"Let's save some time here Lieutenant, you forged your transfer orders and lied to get aboard, all so you could get your scanners on the torpedoes your daddy hid from you."

Charlie must have been more angry than she realized as the blond's eyes got larger and the only she got was a meek nod in answer. Charlie had to decide what to do with the Lieutenant, did she tell Kirk and have Carol hauled off the ship for her own safety or did she let Carol stay, as she could use an ally and Carol's skills? Charlie took a deep breath and blew it out, feeling some of the tension leave her and made the decision.

"Alright this is what we're going to do. I won't say anything and you're going to stay out of the way, unless your expertise is needed. Anything you find in your scans you will notify me immediately. This could be both our asses if you're discovered do you understand Lieutenant?"

Carol quickly nodded and seemed relieved that she was going to stay.

"Now continue to work on the torpedoes and contact me as soon as you have something."

"Yes Ma'am and Charlie thank you."

Charlie rolled her eyes but called after the Lieutenant, "Carol, this mission is suicidal and dangerous for both our sakes just keep your head down, and don't call me Ma'am, it makes me sound old."

Carol smiled and gave Charlie a mock salute and moved off to continue her scans. Charlie just shook her head she would never understand Carol's fascination with weapons and anything that could explode but to each her own.

Charlie could use any and all information Carol managed to uncover, while she had been part of the early design phase Marcus had removed her from the project before the plans had been completed. The torpedoes themselves were almost the same design but much larger than they needed to be and Charlie wanted to know why. She began making her way to the bridge and hoped she hadn't just signed her friend's death warrant.

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Charlie had just reached the transporter when a blur of curly hair, swearing in Russian ran past her while trying to straighten a red uniform shirt.

One name popped into Charlie's head, Chekov. It was the only logical conclusion, but why was he moving in the opposite direction of the bridge. Charlie quickly debated, Kirk wouldn't really need her until they reached the neutral zone and the young officer who had almost run her over seemed to be in a slight panic about something, which on a starship was never a good sign.

Charlie followed Chekov to Engineering and it became clear very quickly that he was now in charge. That left the question of where Mr. Scott had gotten too.

Charlie stayed in the background observing as the new Engineering Chief bounced from one side of Engineering to the other, getting reports and giving orders. For someone so obviously young and inexperienced at being in charge, Charlie had to admit Chekov was holding his own.

Charlie checked the engine read outs and everything seemed to be functioning properly. She was distracted when Kirk came over the ship's communications and began to debrief the crew on their mission. He acknowledged Pike's death and Charlie winced in realization that she was allowing an entire crew and more especially friends and colleagues of Pike to think their friend and mentor was dead. She really hoped keeping that secret wouldn't come back to bite her but until both Khan and Marcus were dealt with Pike wasn't safe. With Khan no one was safe until he got his vengeance or he was locked away but with Marcus, Pike had been one of the few higher ranking officers who could and would challenge Marcus's decisions.

Charlie smirked as Kirk paused and then contradicted the orders from Marcus. She couldn't help but feel satisfied, trust Kirk to follow his heart with a little bit of Spock's logic, to do the right thing.

"Alright, let's go get this bastard."

Charlie began to analyze the data on the planet and the last known location of Khan. There was very little chance they would manage to get in and out undetected and that meant they would have to fight. Charlie began forming plans and back up plans and back up plans to those plans, with her knowledge of Khan, Kirk, and her uneasy that Marcus was up to something left Charlie with the distinct feeling that nothing was going to go as planned and she would need to be ready.

Charlie decided she needed to talk to Kirk to tell him some of her ideas on how to capture 'Harrison' and to get a read on where his head was at, justice or revenge.

Charlie had just left Engineering when the Enterprise gave an almighty lurk and dropped out of warp. Alarms shrieked and steam billowed from several places. Charlie hauled herself up off the ground and ran back to Engineering.

"Chekov, did you break my ship?"

Charlie checked the read outs, there was a major breach coming from somewhere but the computer could not pinpoint it. Chekov must have dropped them out of warp to prevent the engine from going critical.

"Shit."

It was not a coincidence that the Enterprise had a malfunction and that they were now stranded in Klingon space. Whatever was wrong with the engine Charlie would bet Marcus had something to do with it. She quickly turned the alarms off, she couldn't hear herself think with them going off let alone communicate with anyone.

"I'm sure Mr. Chekov will have us ready to go by the time we get back."

Charlie was trying to find the breach when she realized what Kirk had said. She shouldn't have been surprised that he would continue with the mission even with the Enterprise sidelined, but damn it, she couldn't be in two places at once. She quickly called one of the engineers over and explained what she had been doing, giving them instructions on how to complete the scan, and how to stop the breach from expanding once they found it.

"Do you understand Ensign?"

"Yes Ma'am."

Charlie nodded and rushed off to find Kirk, she may not be able to stop him from doing something stupid but she could at least go as back up. With the Enterprise stranded until the breach could be secured, their only hope was to go in with a shuttle and hope they found and subdued Khan before the Klingons found and blew them out of the sky.

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"Captain, I would like to volunteer."

"I think we're all full up there Commander, why don't you see what you can do to help in engineering."

Charlie couldn't be sure if Kirk was being truthful about the shuttle being full or trying to prevent her from coming because he didn't trust her skills. Either way it pissed her off.

"Listen Kirk, you have no idea what its like down there, you have no experience with Harrison, how he thinks, how he fights, and you have no experience in dealing with Klingons. Quite frankly, I call bullshit, and whether you like it or not I am your best chance at capturing Harrison alive and escape the planet without being blow out of the sky by Klingons. Now where can I find suitable clothing?"

The look on the Captain's face made it very hard for Charlie to keep a serious no nonsense look on her face. It was very evident that Kirk was not used to someone calling him out and turning the tables on him. His mouth was open slightly and his eyebrows were raised in what Charlie could only assume was disbelief and perhaps amusement. He seemed to come to a decision and passed Charlie a bag. She opened it and pulled out a pair of leather pants, a corset top, and leather jacket in her size.

Where Kirk had got the clothing Charlie was pretty sure she didn't want to know, but it was clear that Kirk had planned on her coming with but had wanted to see what she would do when he denied her. The clothing was good quality and would protect her from the elements but still allow her to move comfortably. Charlie stuffed the clothes back in the bag and nodded her head in thanks to Kirk, moving off to change.

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Charlie was strapping herself in to one of the three seats in the back of the shuttle when she heard Kirk telling two men to change out of their Starfleet uniforms. When they were attacked, there was no if, but when, there could be nothing linking them to Starfleet. Not only to protect Starfleet but also the Enterprise, which was sitting defenseless in the middle of Klingon space. Charlie approved of the method to Kirk's madness. To everyone who didn't know him, he was a wild card, making plans as he went and flying to the seat of his pants, but Charlie could see the intelligence and strategy that Kirk used. While he was a bit of a wild card, who followed his heart and gut more than his head, he also wasn't stupid enough to ignore the talents and skills of his fellow officers. Kirk might be the Captain but each and every crew member had something to contribute and Kirk would use it to his advantage.

Charlie nodded to the two huge men as they crammed themselves into the back of the ship. Kirk, Spock, and Uhura taking the controls at the front, Charlie had to stop herself from smirking, the brain, the heart, and the woman who keep them in check. The shuttle took off and Charlie shook her head, she needed to focus if they were going to capture Khan and make it out alive.

Charlie looked out the shuttle window as they left the docking bay of the Enterprise, and her only thoughts were, 'Into the darkness, into the deep. May they all come back whole on the other side."

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	6. Chapter 6

Hello everyone, sorry for the long break, this summer has been a little nuts and I haven't been in the mood for writing.

Thank you to all who have read, alerted, favored, and reviewed. It means a lot that you are interested in this story and want to see where Charlie and the crew of the Enterprise are headed.

As always the characters and worlds belong to the creators and owners. I just own Charlie.

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The descent down to the planet seemed to go past in the blink of an eye. Charlie caught of glimpse of the dark surface from her seat, and got the distinct impression that they were descending into Hell. A fitting description since they were about to hunt down and capture a Devil.

Charlie snorted at her own thoughts drawing the attention of her seat mates. She ignored them and began to calculate the number of ways that Kirk's plan could fail; she reached 16 before the shuttle shuttered at its reentry into the atmosphere of Qo'nos.

Kirk ordered Spock to scan the surface of the planet and surrounding air space to confirm they had arrived undetected. After five minutes of nothing on the scanners but the old ruins of an ancient city far below on the planet, Charlie let herself relax slightly. So far so good, no one is shooting at them yet, Charlie thought, maybe they would actually make it off this rock in one piece.

Charlie heard Kirk order Sulu to begin transmitting their message to Khan.

"Attention John Harrison, this is Captain Hikaru Sulu…"

It came in loud and clear over the communication system, Charlie had little doubt that Khan would take the challenge, this was after all what he wanted. It was no fluke that he had chosen Qo'nos as his bolt hole, there was little Starfleet could do, they couldn't demand the Klingons to hand him over, that would force them to admit his escape, showing their weakness to a possible enemy. All they could do was send a starship after him, and hope that the Captain and crew wouldn't spark an interplanetary conflict.

Charlie just couldn't figure out why Khan would leave Earth and his enemy, Marcus. Charlie knew Khan's very nature would force him to plan for every contingent before he made his first move. So why flee half way across a galaxy, when you had the advantage and your enemy was reeling from two major attacks. Khan wasn't stupid; he knew Marcus wouldn't come after him himself, so why did he want to draw a starship so far way from Earth, what could he possibly want?

Charlie mulled over the mystery that was Khan's mind, trying to figure out what she could have missed that could clue her into this complex and deadly game Khan and Marcus seemed to be playing, using her and the Enterprise as pawns.

"…if you test me, you will fail."

Charlie couldn't help but be impressed at the conviction and authority Sulu managed to convey. He would make a good leader one day; she just hoped that they all lived to see it.

The two minutes Sulu had given Khan to respond quickly ran out and still nothing indicating Khan's position. Charlie knew they would have to be patient, they had set the bait now they would have to wait, Khan wouldn't reveal himself if he thought he had the advantage.

Charlie could hear Uhura getting worked up about something; she wondered which one of the men had managed to piss the language expert off.

"You didn't seem to care."

Could have been either one of them with that kind of comment but as Charlie listened to the conversation it became clear that Spock was the target. Charlie didn't know what had prompted the Lieutenant to unleash her emotional tirade on the half-Vulcan, but they didn't have time for this. Personal stuff needed to be dealt with, she would never deny that but not when you are on a mission on a hostile world, trying to capture a man more intelligent and skilled then you were. Charlie wasn't arrogant or stupid enough to underestimate Khan's skills and genius or her own short comings, but once you acknowledge them you can you use them to your advantage. And Charlie would use hers to her full advantage.

Charlie released the straps holding her in the seat, gaining a weird look from her seat mates, and made her way to the front of the shuttle, she managed two steps before she was thrown off her feet and into the wall.

"What the hell was that?"

Charlie struggled to her feet and pausing a few seconds as the inside of the shuttle seemed to spin around her. She groaned as she raised a hand to her head, feeling a large knot beginning to form at her temple.

"Klingons!" Kirk yelled back, making Charlie's head ache more.

"This ship has no offensive capabilities."

"It's got us; give me all six fuel cells."

"Aye, Captain."

Charlie had finally managed to get into the cockpit and had braced herself between Uhura's and Spock's chairs. She clung tightly to the back of Kirk's chair as he maneuvered the ship in between the Klingon's ships avoiding their continual weapons fire and the structures of the planet. Had Charlie not been focusing on trying to stay up right she would have been impressed by Kirk's piloting skills.

"Commander Archer it is unwise and unsafe for you to be out of your seat, please return at this time."

Charlie quickly glanced back at Spock, "Is that an order Commander?"

Spock must have heard something in her tone because he was smart enough not respond.

"Yeah, didn't think so."

There was a near miss almost sending Charlie off her feet again.

"Commander."

Charlie and Spock both looked back to the two men looking at little green at the back of the shuttle, one was holding something in his hand.

"Here, this might help."

He tossed the object to Charlie, it was a harness with a portable rigging system attached, she quickly attached the rigging to the back of Kirk's chair and looped the harness around her waist, probably not the safest but it would keep her from been thrown around and still allow her to move.

Charlie knew she was being a backseat driver but Kirk didn't seem to mind, as he followed her suggestions and managed to keep them from being blown out of the sky.

"Kirk, double back see if you can't lose them."

Charlie clung to the back of Kirk's chair as he did a complete 180 without slowing down and flew head on into the enemy. The Klingons hadn't been expecting their prey to turn on them so the ship barely managed to get out of the way to avoid the income ship.

"Two more head this way, Kirk you have to get us out of here," Uhura was manning the sensors as Spock tried to manipulate the engines into giving up more power.

Kirk swung them back around, they hadn't managed to get rid of any of their pursuers but the maneuver had managed to give them more distant between them.

Charlie was leaning over Spock's shoulder trying to help him boost the engines, when the shuttle shook violently.

"Damnit."

The shuttle continued to weave in and out of the ancient structures, just barely avoiding the Klingon's weapons fire.

"They're closing fast, bearing 2.85."

"There… right there… we can lose them there."

Charlie and Spock whipped their heads up to see what Kirk was talking about, only to see a vertical passage between to massive structures, a very, very narrow vertical passage.

Spock was the first one to respond, "If you are suggesting we utilize the passage between the two approaching structures, this ship will not fit."

"Will fit."

"Captain, we will not fit."

The two structures and passage got closer and closer.

"Shit," Charlie threw herself the floor wedging herself between Kirk's chair and the console and braced her feet against the back of Spock's, hoping against hope that it would be enough that when Kirk ignored Spock's warnings and continued his suicidal maneuver, she would be thrown across the ship.

"Will fit… will fit."

It seemed to be in slow motion, as they seemed to speed up as Kirk flipped the shuttle on its side and piloted it into the gap. They were thrown around as the shuttle bounced off the walls.

Uhura let out a small scream as the grinding and sparks increased every time the shuttle made contact. Charlie too focused on not throwing up or losing her position and falling on Spock to make any comments.

What seemed to last forever, was really only seconds and they were finally free of the passage. They all breathed a sigh of relief that they weren't dead, and Charlie slowly started to pull herself up off the floor.

"I told you we'd fit."

Charlie couldn't help but roll her eyes, at Kirk's comment, as she struggled to remain up right.

"I am not sure that qualifies."

Charlie couldn't stop herself from snorting at Spock's retort. She reached over and patted Kirk on the head.

"Good job, just don't do that again."

Kirk let out a chuckle in agreement, "Let's get out of here and see if we can't find Khan."

The last word hadn't let Kirk's mouth when a bright light blinded them and the sensors began shrilling proximity alerts. They were surrounded by four Klingon ship and there was no way out. Charlie sighed, so much for leaving in one piece.

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